Diseases caused by single gene defects such as Mucolipidosis Type IV (MLIV) present a significant challenge for effective therapy. MLIV, an autosomal recessive neurological disease, is due to defects in the mucolipin gene (MCOLN1) that result in functional loss of the encoded channel pore protein. Because replacement strategies such as gene therapy or recombinant protein delivery are not viable strategies, alternatives are needed. A promising approach is to determine which other genes exhibit altered expression as a result of mucolipin deficiency in order to select druggable targets for therapeutic development. Methods for gene expression profiling have typically involved measurements of accumulated RNA, i.e., RNA profiling that may involve high volume microarrays or smaller numbers of genes by reverse transcriptase PCR. While useful, RNA assays cannot distinguish between transcriptional and posttranscriptional regulation, and exhibit high levels of variability. During Phase I of this project, a novel method called TranscriptionPath was developed to directly measure transcriptional activities of genes by identifying and quantifying complexes containing genomic DNA and transcription-associated proteins. In the proposed Phase II studies, TranscriptionPath will be applied to 3 model systems reproducing key aspects of the MLIV disease: (1) siRNA inhibition of mucolipin gene expression in vitro, including in neuronal cell lines, (2) recreation of MLIV defects by modulating intracellular Ca2+ levels, and (3) testing of MCOLN1 knock-out mice. The combined approach will generate a list of candidate genes that can be further developed into therapeutic targets and/or diagnostic biomarkers. The proposed methods will also be applicable to other genetic neurological disorders for which in vitro or animal models exist. Relevance: There are more than 600 neurological disorders, many of which have a genetic component. Even though many of these disorders are orphan or rare diseases, together they represent an important and significant health issue. Methods are proposed that make use of a common characteristic of such disorders, i.e., altered gene expression, to work toward therapies for many of these diseases.